CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1

Abstract

The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:A) Qiime – a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;B) UCHIME – a tool for rapid identification of chimeric 16S sequence fragments;C) Mothur – a C++-based software package for 16S analysis;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.CloVR-16S accepts as input raw multiplex 454-pyrosequencer output (i.e. pooled pyrotagged sequences from multiple samples), or alternatively, pre-processed sequences from multiple samples in separate files. This protocol became first available in CloVR beta version 0.7.